Abstract
BackgroundRNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs.ResultsSince its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structural-alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures into one-dimensional (1D) structural sequences and applies BLAST to the resulting structural sequences for searching similar substructures of RNAs. In this study, we have upgraded R3D-BLAST to develop a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept an RNA structure in the mmCIF format as an input. The results of our experiments on a benchmark dataset have demonstrated that R3D-BLAST2 indeed performs very well in comparison to its earlier version R3D-BLAST and other similar tools RNA FRABASE, FASTR3D and RAG-3D by searching a larger number of RNA 3D substructures resembling those of the input RNA.ConclusionsR3D-BLAST2 is a valuable BLAST-like search tool that can more accurately scan the PDB database for similar RNA 3D substructures. It is publicly available at http://genome.cs.nthu.edu.tw/R3D-BLAST2/.
Highlights
RNA molecules have been known to play a variety of significant roles in cells
The above method we used to implement R3D-BLAST [8] is the so-called structural alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures from the Protein Data Bank (PDB) database into 1D sequences of structural letters and continues to apply BLAST [10], a popular bioinformatics tool to find homologous nucleotide or amino acid sequences just according to their sequence similarity, to search the SA-encoded sequences for similar RNA 3D substructures
We collected 63 402 non-terminal nucleotides from a representative and sufficiently non-redundant list of 876 RNA 3D structures determined by X-ray crystallography and electron microscopy from the RNA 3D Hub [14] and applied the affinity propagation (AP) algorithm [15] to classify these nucleotides into 23 conformation clusters using their η and θ values
Summary
RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. In the past few years, both the number and the size of experimentally solved RNA 3D structures in the Protein Data Bank (PDB) [2]. In principle, both RNA FRABASE and FASTR3D use pattern-based approaches to search the PDB database for RNAs that have exactly the same secondary (2D) structure as that of the query RNA. Yen et al BMC Bioinformatics 2017, 18(Suppl 16):574 reduces RNA 3D structures into one-dimensional (1D) structural sequences according to some local structure features in the nucleotide backbone conformation and applies BLAST to the resulting 1D structural sequences for searching similar RNA 3D substructures. It can be expected that these newly determined RNA 3D structures should allow us to construct a new and sufficiently highquality SA that can be used to further improve the search performance of R3D-BLAST
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